Mercurial > repos > jjohnson > qiime
comparison exclude_seqs_by_blast.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="exclude_seqs_by_blast" name="exclude_seqs_by_blast" version="1.2.0"> | |
| 2 <description>Exclude contaminated sequences using BLAST</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">exclude_seqs_by_blast.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 exclude_seqs_by_blast.py | |
| 10 --querydb=$querydb | |
| 11 --subjectdb=$subjectdb | |
| 12 --outputfilename=$outputfilename | |
| 13 --e_value=$e_value | |
| 14 --percent_aligned=$percent_aligned | |
| 15 $no_clean | |
| 16 --blastmatroot=$blastmatroot | |
| 17 --working_dir=$working_dir | |
| 18 --max_hits=$max_hits | |
| 19 --word_size=$word_size | |
| 20 $no_format_db | |
| 21 </command> | |
| 22 <inputs> | |
| 23 <param name="querydb" type="text" label="querydb" | |
| 24 help="The path to a FASTA file containing query sequences [REQUIRED]"/> | |
| 25 <param name="subjectdb" type="text" label="subjectdb" | |
| 26 help="The path to a FASTA file to BLAST against [REQUIRED]"/> | |
| 27 <param name="e_value" type="float" value="1e-10" label="e_value" | |
| 28 help="The e-value cutoff for blast queries [default: 1e-10]."/> | |
| 29 <param name="percent_aligned" type="float" value="0.97" label="percent_aligned" | |
| 30 help="The % alignment cutoff for blast queries [default: 0.97]."/> | |
| 31 <param name="no_clean" type="boolean" truevalue="--no_clean" falsevalue="" checked="false" label="no_clean" | |
| 32 help="If set, don't delete files generated by formatdb after running [default: False]."/> | |
| 33 <param name="blastmatroot" type="text" label="blastmatroot" | |
| 34 help="Path to a folder containing blast matrices [default: %default]."/> | |
| 35 <param name="working_dir" type="text" value="/tmp" label="working_dir" | |
| 36 help="Working dir for BLAST [default: /tmp]."/> | |
| 37 <param name="max_hits" type="integer" value="100" label="max_hits" | |
| 38 help="Max hits parameter for BLAST. CAUTION: Because filtering on alignment percentage occurs after BLAST, a max hits value of 1 in combination with an alignment percent filter could miss valid contaminants. [default: 100]"/> | |
| 39 <param name="word_size" type="integer" value="28" label="word_size" | |
| 40 help="Word size to use for BLAST search [default: 28]"/> | |
| 41 <param name="no_format_db" type="boolean" truevalue="--no_format_db" falsevalue="" checked="false" label="no_format_db" | |
| 42 help="If this flag is specified, format_db will not be called on the subject database (formatdb will be set to False). This is useful if you have already formatted the database and a) it took a very long time or b) you want to run the script in parallel on the pre-formatted database [default: False]"/> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="txt" name="outputfilename"/> | |
| 46 </outputs> | |
| 47 <tests> | |
| 48 </tests> | |
| 49 <help> | |
| 50 | |
| 51 </help> | |
| 52 </tool> | |
| 53 |